Skip to content

Commit

Permalink
Update README and Get started
Browse files Browse the repository at this point in the history
  • Loading branch information
adamkucharski committed Jan 15, 2024
1 parent 120a415 commit 5bba24d
Show file tree
Hide file tree
Showing 2 changed files with 4 additions and 2 deletions.
4 changes: 2 additions & 2 deletions README.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -26,9 +26,9 @@ knitr::opts_chunk$set(

_{{ packagename }}_ is an R package to calculate the final size of a SIR epidemic in populations with heterogeneity in social contacts and infection susceptibility.

_{{ packagename }}_ provides estimates for the total proportion of a population infected over the course of an epidemic, and can account for a demographic distribution (such as age groups) and demography-specific contact patterns, as well as for heterogeneous susceptibility to infection between groups (such as due to age-group specific immune responses) and within groups (such as due to immunisation programs).
_{{ packagename }}_ provides estimates for the total proportion of a population infected over the course of an epidemic, and can account for a demographic distribution (such as age groups) and demography-specific contact patterns, as well as for heterogeneous susceptibility to infection between groups (such as due to age-group specific immune responses) and within groups (such as due to immunisation programs). An advantage of this approach is that it requires fewer parameters to be defined compared to a model that simulates the full transmission dynamics over time, such as models in the [_epidemics_ package](https://epiverse-trace.github.io/epidemics/articles/epidemics.html).

_{{ packagename }}_ implements methods outlined in @andreasen2011, @miller2012, @kucharski2014, and @bidari2016.
_{{ packagename }}_ implements methods outlined in @andreasen2011, @miller2012, @kucharski2014, and @bidari2016.

_{{ packagename }}_ can help provide rough estimates of the effectiveness of pharmaceutical interventions in the form of immunisation programmes, or the effect of naturally acquired immunity through previous infection (see the vignette).

Expand Down
2 changes: 2 additions & 0 deletions vignettes/finalsize.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,8 @@ vignette: >
When analysing an epidemic-prone infection, such as pandemic influenza, it is important to understand how many infections there could be in total. The overall number of infections that occur during such an epidemic, is called the 'final epidemic size'.
The expected final size of an epidemic can be calculated using methods detailed in @andreasen2011, @miller2012, @kucharski2014, and @bidari2016, and which are implemented in the _finalsize_ package.

An advantage of the final size approach is that it is only necessary to define pathogen transmissibility and population susceptibility to calculate the epidemic size, rather than requiring estimates of additional time-dependent processes like the duration of infectiousness or delay from infection to onset of symptoms. So _finalsize_ will be particularly relevant for questions where understanding the overall size of an epidemic is more important than estimating its shape.

::: {.alert .alert-primary}
## Use case {-}

Expand Down

0 comments on commit 5bba24d

Please sign in to comment.